Variant report

Variant	rs2439593
Chromosome Location	chr5:112072889-112072890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr5:112072800-112073081	HL-60	blood:	n/a	n/a
2	MXI1	chr5:112072871-112074773	SK-N-SH	brain:	n/a	n/a
3	RCOR1	chr5:112072853-112074400	K562	blood:	n/a	n/a
4	REST	chr5:112072882-112075247	H1-neurons	neurons:	n/a	chr5:112073638-112073647

No.	Distal block	Cell Line	Cell type
1	chr5:112041577..112049243-chr5:112069735..112074802,8	K562	blood:
2	chr5:112070188..112073138-chr5:112174884..112177444,2	K562	blood:
3	chr5:112041486..112046402-chr5:112068342..112076365,12	K562	blood:
4	chr5:112042397..112044645-chr5:112071738..112074273,3	MCF-7	breast:
5	chr5:112066564..112068742-chr5:112071367..112073488,2	MCF-7	breast:

Variant related genes	Relation type
APC	TF binding region
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11953943	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11960216	0.99[EUR][1000 genomes]
rs1644239	0.81[EUR][1000 genomes]
rs1644241	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1644242	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1661032	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1661034	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1697914	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1697916	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17134960	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1734244	0.93[EUR][1000 genomes]
rs1734245	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1734246	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1734247	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1882619	1.00[GIH][hapmap]
rs2431505	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2431507	0.90[CEU][hapmap];0.95[GIH][hapmap];0.85[EUR][1000 genomes]
rs2431508	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2431509	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2431511	1.00[EUR][1000 genomes]
rs2439590	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2439592	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2439594	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2455294	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2455296	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2464802	0.85[EUR][1000 genomes]
rs2464808	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2464810	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2909784	1.00[EUR][1000 genomes]
rs2909961	1.00[EUR][1000 genomes]
rs2909962	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs73220022	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112054400-112073200	Weak transcription	Pancreas	Pancrea
2	chr5:112059200-112073200	Weak transcription	Left Ventricle	heart
3	chr5:112061000-112073000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:112061800-112073000	Weak transcription	Fetal Stomach	stomach
5	chr5:112062200-112073000	Weak transcription	Brain Germinal Matrix	brain
6	chr5:112062400-112073000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:112062400-112073000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:112065200-112073000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:112067800-112073000	Weak transcription	Psoas Muscle	Psoas
10	chr5:112068200-112073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:112069200-112073000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:112069200-112073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:112069600-112073000	Weak transcription	HMEC	breast
14	chr5:112069800-112073000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:112070000-112073000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:112070000-112073200	Weak transcription	Lung	lung
17	chr5:112070600-112073000	Enhancers	Osteobl	bone
18	chr5:112071200-112073000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:112071200-112073200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:112071600-112073000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr5:112071800-112073000	Enhancers	HSMM	muscle
22	chr5:112072200-112073000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:112072200-112073000	Weak transcription	A549	lung
24	chr5:112072400-112073000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:112072400-112073000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:112072400-112073000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:112072400-112073000	Enhancers	Primary B cells from peripheral blood	blood
28	chr5:112072400-112073000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr5:112072400-112073000	Enhancers	Thymus	Thymus
30	chr5:112072600-112073000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr5:112072600-112073000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:112072600-112073000	Enhancers	Colon Smooth Muscle	Colon
33	chr5:112072600-112073200	Weak transcription	Spleen	Spleen
34	chr5:112072600-112074000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:112072600-112074200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr5:112072600-112074400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:112072600-112074600	Flanking Active TSS	Dnd41	blood
38	chr5:112072800-112073000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr5:112072800-112073000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:112072800-112073000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr5:112072800-112073000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr5:112072800-112073000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:112072800-112073000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr5:112072800-112073000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:112072800-112073000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr5:112072800-112073000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:112072800-112073000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:112072800-112073000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:112072800-112073000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:112072800-112073000	Flanking Active TSS	Adipose Nuclei	Adipose

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